Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016743.1 Corchorus olitorius cultivar O-4 contig16776, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 50156
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:1750 original size:15 final size:15
Alignment explanation
Indices: 1730--1760 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1720 TTCAATAAAA
*
1730 TAATAATTATTTAAT
1 TAATAATTAATTAAT
1745 TAATAATTAATTAAT
1 TAATAATTAATTAAT
1760 T
1 T
1761 TCAACCCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATAATTAATTAAT
Found at i:1755 original size:19 final size:18
Alignment explanation
Indices: 1707--1757 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
1697 TGTAGGATTT
1707 TTAATAATAATTATTCAA
1 TTAATAATAATTATTCAA
* *
1725 TAAAATAATAATTATTTAA
1 T-TAATAATAATTATTCAA
1744 TTAATAATTAATTA
1 TTAATAA-TAATTA
1758 ATTTCAACCC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
TTAATAATAATTATTCAA
Found at i:11512 original size:3 final size:3
Alignment explanation
Indices: 11504--11551 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
11494 TCTCCTATCA
11504 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CATT -TT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT
11549 CTT
1 CTT
11552 TGATCAACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:11723 original size:9 final size:9
Alignment explanation
Indices: 11709--11776 Score: 136
Period size: 9 Copynumber: 7.6 Consensus size: 9
11699 AGAAAGCCCA
11709 GCTGCCGCC
1 GCTGCCGCC
11718 GCTGCCGCC
1 GCTGCCGCC
11727 GCTGCCGCC
1 GCTGCCGCC
11736 GCTGCCGCC
1 GCTGCCGCC
11745 GCTGCCGCC
1 GCTGCCGCC
11754 GCTGCCGCC
1 GCTGCCGCC
11763 GCTGCCGCC
1 GCTGCCGCC
11772 GCTGC
1 GCTGC
11777 TGGTGGGTGG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 59 1.00
ACGTcount: A:0.00, C:0.54, G:0.34, T:0.12
Consensus pattern (9 bp):
GCTGCCGCC
Found at i:18925 original size:134 final size:132
Alignment explanation
Indices: 18676--18925 Score: 315
Period size: 134 Copynumber: 1.9 Consensus size: 132
18666 TATCTAAGTT
18676 TAGTAAAATGATAAAAATAAAATAGGTATAAGGATATTAGATATAATTAAATAAAAAATAGAGTT
1 TAGTAAAATGATAAAAATAAAATAGGTATAAGGATATTAGATATAATTAAATAAAAAATAGAGTT
* *** ** *
18741 TTTAGTTGAGTAAAACTATAAAAGTATATTTAAAAAATTCTATTATATATAATTTTTTTAATTAA
66 TTTAGTTGAGTAAAACTATAAAAATATAAACAAAAAATTCTAAGAAATATAATTTTTTTAATTAA
18806 AA
131 AA
* * * * *
18808 TAGTAAAATGGTAAAAATTAAATAGTTATAAGGATAATATTAGATTTAATTAAA-CAAAAATAGA
1 TAGTAAAATGATAAAAATAAAATAGGTATAAGG---ATATTAGATATAATTAAATAAAAAATAGA
* **
18872 GTTTTTAGTTGAGTAAAACTATAAAAATCTAAACAATAGCATT-TAAGAAATATA
63 GTTTTTAGTTGAGTAAAACTATAAAAATATAAACAA-AAAATTCTAAGAAATATA
18926 TTCGAAAAAT
Statistics
Matches: 99, Mismatches: 15, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
132 30 0.30
134 48 0.48
135 21 0.21
ACGTcount: A:0.52, C:0.03, G:0.11, T:0.35
Consensus pattern (132 bp):
TAGTAAAATGATAAAAATAAAATAGGTATAAGGATATTAGATATAATTAAATAAAAAATAGAGTT
TTTAGTTGAGTAAAACTATAAAAATATAAACAAAAAATTCTAAGAAATATAATTTTTTTAATTAA
AA
Found at i:21137 original size:64 final size:64
Alignment explanation
Indices: 21024--21152 Score: 213
Period size: 64 Copynumber: 2.0 Consensus size: 64
21014 CTAATAGTCT
* * *
21024 ACCAAAAAGTCTTTTCAAATATAGAAATAATCTTGAAAAGTAAGTACAAAAAATGTCAATCTCG
1 ACCAAAAAGTCTCTTCAAATATAGAAATAATCTTGAAAACTAAGAACAAAAAATGTCAATCTCG
* *
21088 ACCAGAAAGTCTCTTCAAATATAGATATAATCTTGAAAACTAAGAACAAAAAATGTCAATCTCG
1 ACCAAAAAGTCTCTTCAAATATAGAAATAATCTTGAAAACTAAGAACAAAAAATGTCAATCTCG
21152 A
1 A
21153 AAAATTTGGG
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.26
Consensus pattern (64 bp):
ACCAAAAAGTCTCTTCAAATATAGAAATAATCTTGAAAACTAAGAACAAAAAATGTCAATCTCG
Found at i:21598 original size:219 final size:218
Alignment explanation
Indices: 21135--22026 Score: 1303
Period size: 219 Copynumber: 4.2 Consensus size: 218
21125 AACTAAGAAC
* * * *
21135 AAAAAATGTCAATCTC-GAAAAATTTGGGTAAGGTGCATATGATTATGTGGAGATGATGAGAAAT
1 AAAAAATGTCAATCTCTAAAAAATTTGGGGATGGTGCATATGATTATGTGGGGATGATGAGAAAT
* * * *
21199 GATTTGGGTATGAAGTATATCAGTTTGGAGATACTGAATTTTGCATTTTGTTTAATTATTAGATG
66 GATTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGCATGTTGTTTAATTATTAGATG
* *
21264 GCACAAAATTCATATAGA-TAGGGTTTATTCAATTAATT-GTGATGAAAATATGGATTAAAACAC
131 ACACTAAATTCATATAGACT-GGGTTTATTCAATTAATTAG-GATGAAAATATGGATTAAAACAC
* *
21327 GTTTAAAACCAATTTTGGGTATATA
194 GTTTAAAGCCAATTTTGGGCATATA
* *
21352 AAAAAATGTCAATCCCTAAAGAATTTGGGGATGGTGCATATGATTATGTGGGGATGATGAGAAAT
1 AAAAAATGTCAATCTCTAAAAAATTTGGGGATGGTGCATATGATTATGTGGGGATGATGAGAAAT
21417 GATTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGCATGTTGTTTAATTATTAGATT
66 GATTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGCATGTTGTTTAATTATTAGA-T
* *
21482 GACACTAAATTCATATAGACTGGGTTTATTCAATTAATCAGGATGAAAATATGGATTAAAACACA
130 GACACTAAATTCATATAGACTGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACG
*
21547 TTTAAAGTCAATTTTGGGCATATA
195 TTTAAAGCCAATTTTGGGCATATA
* *
21571 AAAAAATGTCAATCTCTAAAAAATTTGGGGATGGTGCATATGATTATATGAGGATGATGAGAAAT
1 AAAAAATGTCAATCTCTAAAAAATTTGGGGATGGTGCATATGATTATGTGGGGATGATGAGAAAT
*
21636 GATTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGCATGTTCTTTAATTATTAGATG
66 GATTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGCATGTTGTTTAATTATTAGATG
* *
21701 --AC---A--C---T--ACT-GGTTTATTCAATTAATTAAGATGAAAATATGGATTAAAGCACGT
131 ACACTAAATTCATATAGACTGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACGT
*
21753 TTAAAGCCAATTTTGGGTATATA
196 TTAAAGCCAATTTTGGGCATATA
* * * *
21776 AAAAAATGTCAATCTCGAAAACATTTGGGGATGGTGCAAATGATTATTTGGGGATGATGAGAAAT
1 AAAAAATGTCAATCTCTAAAAAATTTGGGGATGGTGCATATGATTATGTGGGGATGATGAGAAAT
* * * * *
21841 GAGTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGTATTTTGTTTAACTATTAGATG
66 GATTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGCATGTTGTTTAATTATTAGATG
* * * *
21906 ACACTAAATTCATATAGACAGGGTTTATTCAAATAATTAGGATGAAAATATGGATTAAAGCATGT
131 ACACTAAATTCATATAGACTGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACGT
*
21971 TTAAAGTCAATTTTGGGCATATA
196 TTAAAGCCAATTTTGGGCATATA
*
21994 AAAAAATGTCAATCTCTAAAAATTTTGGGGATG
1 AAAAAATGTCAATCTCTAAAAAATTTGGGGATG
22027 ATGTGAAATG
Statistics
Matches: 610, Mismatches: 48, Indels: 33
0.88 0.07 0.05
Matches are distributed among these distances:
205 180 0.30
206 3 0.00
207 2 0.00
208 1 0.00
210 1 0.00
211 1 0.00
212 1 0.00
213 1 0.00
215 1 0.00
216 2 0.00
217 17 0.03
218 196 0.32
219 202 0.33
220 2 0.00
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.35
Consensus pattern (218 bp):
AAAAAATGTCAATCTCTAAAAAATTTGGGGATGGTGCATATGATTATGTGGGGATGATGAGAAAT
GATTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGCATGTTGTTTAATTATTAGATG
ACACTAAATTCATATAGACTGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACGT
TTAAAGCCAATTTTGGGCATATA
Found at i:21856 original size:205 final size:203
Alignment explanation
Indices: 21504--22298 Score: 766
Period size: 205 Copynumber: 3.9 Consensus size: 203
21494 ATATAGACTG
* * * *
21504 GGTTTATTCAATTAATCAGGATGAAAATATGGATTAAAACACATTTAAAGTCAATTTTGGGCATA
1 GGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAGCACGTTTAAAGCCAATTTTGGGCATA
* * *
21569 TAAAAAAATGTCAATCTCTAAAAAATTTGGGGATGGTGCATATGATTATATGAGGATGATGAGAA
66 TAAAAAAATGTCAATCTCT-AAAAATTTGGGGATGGTGCAAATGATTATTTGGGGATGATGAGAA
*
21634 ATGATTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGCATGTTCTTTAATTATTAGA
130 ATGAGTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGCATGTTCTTTAA-TATTAGA
21699 TGACACTACT
194 TGACACTACT
* *
21709 GGTTTATTCAATTAATTAAGATGAAAATATGGATTAAAGCACGTTTAAAGCCAATTTTGGGTATA
1 GGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAGCACGTTTAAAGCCAATTTTGGGCATA
*
21774 TAAAAAAATGTCAATCTCGAAAACATTTGGGGATGGTGCAAATGATTATTTGGGGATGATGAGAA
66 TAAAAAAATGTCAATCTCTAAAA-ATTTGGGGATGGTGCAAATGATTATTTGGGGATGATGAGAA
* * * *
21839 ATGAGTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGTATTTTGTTTAACTATTAGA
130 ATGAGTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGCATGTTCTTTAA-TATTAGA
21904 TGACACTAAATTCATAT
194 TGACACT--A--C---T
* * *
21921 AGACAGGGTTTATTCAAATAATTAGGATGAAAATATGGATTAAAGCATGTTTAAAGTCAATTTTG
1 ------GGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAGCACGTTTAAAGCCAATTTTG
*
21986 GGCATATAAAAAAATGTCAATCTCTAAAAATTTTGGGGATGATGTG-AAATG---ATTTGGGTAT
60 GGCATATAAAAAAATGTCAATCTCTAAAAA-TTTGGGGATG--GTGCAAATGATTATTTGGGGAT
* * * * * * * * *
22047 -A-AAGTATATCAGTTTGGGGATACTGAATTTTGT-A-TTT--TG-T--TTAATTATTAG-ATG-
122 GATGAG-AAATGAG-TT-GGG-TA-TAAAGTATATCACTTTGGGGATACTGAATT-TT-GCATGT
* ** * * * *
22101 ACACTAA-ATT-CAT-ATA-GACG
180 TCTTTAATATTAGATGACACTACT
*
22121 GAGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAGCACGTTTAAAGCCAATTTTGGGTAT
1 G-GTTTATTCAATTAATTAGGATGAAAATATGGATTAAAGCACGTTTAAAGCCAATTTTGGGCAT
* * ** *
22186 ATAAGATAAGATGTCAATCTCTAATGAATTTGGGGATGGTGCTTATGATTATTTGGGAATGATGA
65 ATAA-A-AAAATGTCAATCTCTAA-AAATTTGGGGATGGTGCAAATGATTATTTGGGGATGATGA
* * **
22251 G-AATGATTTGGGTATAGAGTATATCACTTTGGGGATGTTGAATTTTGC
127 GAAATGAGTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGC
22299 GCATGCCTCA
Statistics
Matches: 487, Mismatches: 61, Indels: 88
0.77 0.10 0.14
Matches are distributed among these distances:
194 1 0.00
195 71 0.15
196 7 0.01
197 32 0.07
198 4 0.01
199 13 0.03
200 3 0.01
201 4 0.01
202 5 0.01
203 1 0.00
204 4 0.01
205 182 0.37
207 1 0.00
208 2 0.00
209 3 0.01
210 3 0.01
212 9 0.02
213 4 0.01
214 4 0.01
215 7 0.01
216 11 0.02
217 7 0.01
218 95 0.20
219 11 0.02
220 3 0.01
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.36
Consensus pattern (203 bp):
GGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAGCACGTTTAAAGCCAATTTTGGGCATA
TAAAAAAATGTCAATCTCTAAAAATTTGGGGATGGTGCAAATGATTATTTGGGGATGATGAGAAA
TGAGTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGCATGTTCTTTAATATTAGATG
ACACTACT
Found at i:22067 original size:195 final size:197
Alignment explanation
Indices: 21821--22223 Score: 679
Period size: 195 Copynumber: 2.1 Consensus size: 197
21811 GCAAATGATT
21821 ATTTGGGGATGATGAGAAATGAGTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGTA
1 ATTTGGGGATGATGAGAAATGAGTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGTA
21886 TTTTGTTTAACTATTAGATGACACTAAATTCATATAGACAGG-GTTTATTCAAATAATTAGGATG
66 TTTTGTTTAACTATTAGATGACACTAAATTCATATAGAC-GGAGTTTATTCAAATAATTAGGATG
* *
21950 AAAATATGGATTAAAGCATGTTTAAAGTCAATTTTGGGCATATAA-A-AAAATGTCAATCTCTAA
130 AAAATATGGATTAAAGCACGTTTAAAGCCAATTTTGGGCATATAAGATAAAATGTCAATCTCTAA
22013 -AA
195 TAA
* *
22015 ATTTTGGGGATGATGTGAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGT
1 A-TTTGGGGATGATGAGAAATGAGTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGT
* *
22080 ATTTTGTTTAATTATTAGATGACACTAAATTCATATAGACGGAGTTTATTCAATTAATTAGGATG
65 ATTTTGTTTAACTATTAGATGACACTAAATTCATATAGACGGAGTTTATTCAAATAATTAGGATG
* *
22145 AAAATATGGATTAAAGCACGTTTAAAGCCAATTTTGGGTATATAAGATAAGATGTCAATCTCTAA
130 AAAATATGGATTAAAGCACGTTTAAAGCCAATTTTGGGCATATAAGATAAAATGTCAATCTCTAA
*
22210 TGA
195 TAA
22213 ATTTGGGGATG
1 ATTTGGGGATG
22224 GTGCTTATGA
Statistics
Matches: 195, Mismatches: 9, Indels: 7
0.92 0.04 0.03
Matches are distributed among these distances:
194 3 0.02
195 163 0.84
196 1 0.01
197 26 0.13
198 2 0.01
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (197 bp):
ATTTGGGGATGATGAGAAATGAGTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGTA
TTTTGTTTAACTATTAGATGACACTAAATTCATATAGACGGAGTTTATTCAAATAATTAGGATGA
AAATATGGATTAAAGCACGTTTAAAGCCAATTTTGGGCATATAAGATAAAATGTCAATCTCTAAT
AA
Found at i:22172 original size:424 final size:415
Alignment explanation
Indices: 21184--22298 Score: 1537
Period size: 424 Copynumber: 2.7 Consensus size: 415
21174 TGATTATGTG
* * *
21184 GAGATGATGAGAAATGATTTGGGTATGAAGTATATCAGTTTGGAGATACTGAATTTTGCATTTTG
1 GAGATGATGTGAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGCATTTTG
* *
21249 TTTAATTATTAGATGGCACAAAATTCATATAGATAGGGTTTATTCAATTAATT-GTGATGAAAAT
66 TTTAATTATTAGATGACACTAAATTCATATAG--AGGGTTTATTCAATTAATTAG-GATGAAAAT
* * *
21313 ATGGATTAAAACACGTTTAAAACCAATTTTGGGTATATAAAAAAATGTCAATCCCTAAAGAATTT
128 ATGGATTAAAGCACGTTTAAAGCCAATTTTGGGTATATAAAAAAATGTCAATCTCTAAA-AATTT
*
21378 GGGGATGGTGCATATGATTATGTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCACTTT
192 GGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCACTTT
* *
21443 GGGGATACTGAATTTTGCATGTTGTTTAATTATTAGATTGACACTAAATTCATATAGACTGGGTT
257 GGGGATACTGAATTTTGCATGTTGTTTAACTATTAGATTGACACTAAATTCATATAGACAGGGTT
*
21508 TATTCAATTAATCAGGATGAAAATATGGATTAAAACACATTTAAAGTCAATTTTGGGCATATAAA
322 TATTCAAATAATCAGGATGAAAATATGGATTAAAACACATTTAAAGTCAATTTTGGGCATATAAA
21573 AAAATGTCAATCTCTAAAAAATTTGGGGATGGT
387 AAAATGTCAATCTCTAAAAAATTT---G-TGGT
*
21606 GCATATGATTATATGAGGATGATGAGAAATGATTTGGGTATAAAGTATATCACTTTGGGGATACT
1 G---A-G-----AT---GATG-T--GAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACT
* *
21671 GAATTTTGCATGTTCTTTAATTATTAGATGACACT--A--C---T----GGTTTATTCAATTAAT
51 GAATTTTGCATTTTGTTTAATTATTAGATGACACTAAATTCATATAGAGGGTTTATTCAATTAAT
*
21725 TAAGATGAAAATATGGATTAAAGCACGTTTAAAGCCAATTTTGGGTATATAAAAAAATGTCAATC
116 TAGGATGAAAATATGGATTAAAGCACGTTTAAAGCCAATTTTGGGTATATAAAAAAATGTCAATC
* * *
21790 TCGAAAACATTTGGGGATGGTGCAAATGATTATTTGGGGATGATGAGAAATGAGTTGGGTATAAA
181 TCTAAAA-ATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAA
* * *
21855 GTATATCAGTTTGGGGATACTGAATTTTGTATTTTGTTTAACTATTAGA-TGACACTAAATTCAT
245 GTATATCACTTTGGGGATACTGAATTTTGCATGTTGTTTAACTATTAGATTGACACTAAATTCAT
* * **
21919 ATAGACAGGGTTTATTCAAATAATTAGGATGAAAATATGGATTAAAGCATGTTTAAAGTCAATTT
310 ATAGACAGGGTTTATTCAAATAATCAGGATGAAAATATGGATTAAAACACATTTAAAGTCAATTT
21984 TGGGCATATAAAAAAATGTCAATCTCT-AAAAATTT-TGG-
375 TGGGCATATAAAAAAATGTCAATCTCTAAAAAATTTGTGGT
*
22022 G-GATGATGTGAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGTATTTTG
1 GAGATGATGTGAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGCATTTTG
22086 TTTAATTATTAGATGACACTAAATTCATATAGACGGAGTTTATTCAATTAATTAGGATGAAAATA
66 TTTAATTATTAGATGACACTAAATTCATATAGA-GG-GTTTATTCAATTAATTAGGATGAAAATA
* *
22151 TGGATTAAAGCACGTTTAAAGCCAATTTTGGGTATATAAGATAAGATGTCAATCTCTAATGAATT
129 TGGATTAAAGCACGTTTAAAGCCAATTTTGGGTATATAA-A-AAAATGTCAATCTCTAA-AAATT
* * *
22216 TGGGGATGGTGCTTATGATTATTTGGGAATGATGAG-AATGATTTGGGTATAGAGTATATCACTT
191 TGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCACTT
**
22280 TGGGGATGTTGAATTTTGC
256 TGGGGATACTGAATTTTGC
22299 GCATGCCTCA
Statistics
Matches: 617, Mismatches: 43, Indels: 74
0.84 0.06 0.10
Matches are distributed among these distances:
400 71 0.12
402 2 0.00
403 4 0.01
404 1 0.00
406 2 0.00
407 1 0.00
411 1 0.00
412 1 0.00
413 66 0.11
414 42 0.07
415 51 0.08
416 2 0.00
417 3 0.00
422 9 0.01
423 102 0.17
424 180 0.29
425 1 0.00
426 1 0.00
430 1 0.00
431 2 0.00
433 1 0.00
434 4 0.01
435 1 0.00
437 68 0.11
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.36
Consensus pattern (415 bp):
GAGATGATGTGAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGCATTTTG
TTTAATTATTAGATGACACTAAATTCATATAGAGGGTTTATTCAATTAATTAGGATGAAAATATG
GATTAAAGCACGTTTAAAGCCAATTTTGGGTATATAAAAAAATGTCAATCTCTAAAAATTTGGGG
ATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCACTTTGGGG
ATACTGAATTTTGCATGTTGTTTAACTATTAGATTGACACTAAATTCATATAGACAGGGTTTATT
CAAATAATCAGGATGAAAATATGGATTAAAACACATTTAAAGTCAATTTTGGGCATATAAAAAAA
TGTCAATCTCTAAAAAATTTGTGGT
Found at i:23160 original size:218 final size:219
Alignment explanation
Indices: 22780--24091 Score: 1934
Period size: 218 Copynumber: 6.0 Consensus size: 219
22770 CTTGATATTA
* * *
22780 CTCATCATCCCCA-ACTAATCATAAGCACCATCCCCAAATTCATTAGACATTGACATTTTTTCTT
1 CTCATCATCCCCACA-TAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTT-TT
*
22844 ATATACCCAAAATTGGCTTTAAACGTGCTTTAATCCGTATTTTCATCCTAATTAATTGAATAAAC
64 ATATACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAAC
** * * * * * **
22909 CTAGTCTAAATGAATTTAGTGCCATCTAATAATTAAACAACATGCAAAATTCAGTATTCCCAAGG
129 CCCGTCTATATGAATTTTGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAC
22974 TGATATACTTTATACCCAAATCATTT
194 TGATATACTTTATACCCAAATCATTT
*
23000 CTCATCATCCCCACATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGGCA-TTTTTTTAT
1 CTCATCATCCCCACATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTTTAT
* * * * *
23064 ATACCCAAAATTGGGTTTAAACATGTTTTAATCTATATTTTCATCCTAATTAATTGAATAAACCA
66 ATACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCC
* * * * *
23129 TGTCTATATGAATTTTGTGTCATTTAATAATTAAACAAAATGTAAAATTCAGTATCTCCAAACTA
131 CGTCTATATGAATTTTGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAACTG
23194 ATATACTTTATACCCAAATCATTT
196 ATATACTTTATACCCAAATCATTT
* *
23218 CTCATAATCCCCACATAATCATATGCATCATCCCCAAATTCTTTAGAGATTGACA-TTTTTTTAT
1 CTCATCATCCCCACATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTTTAT
23282 ATACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCC
66 ATACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCC
* *
23347 CGTCCATATGAATTTTGTGTCATCTAATAATTAAACAAAATGCAATATTCAGTATCCCCAAACTG
131 CGTCTATATGAATTTTGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAACTG
23412 ATATACTTTATACCCAAATCATTT
196 ATATACTTTATACCCAAATCATTT
* * *
23436 CTCATCATCCCCAAATAAACATATGCAACATCCCCAAATTCTTTAGAGATTGACATTTTTTTTAT
1 CTCATCATCCCCACATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTTTAT
* * * * *
23501 ATACCCAAAATTGGGTTTAAACGTGTTTTAATCCATATTTTCGTCCTAATTAATTTAATAAACCA
66 ATACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCC
* * * *
23566 TGTCTATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCAAAATTCAGTATCTCCAAGCTG
131 CGTCTATATGAATTTTGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAACTG
23631 ATATACTTTATACCCAAATCATTT
196 ATATACTTTATACCCAAATCATTT
*
23655 CTCATCATCCCCACATAATCATATGCACCATCCCCAAATTTTTTAGAGATTGACA-TTTTTTTAT
1 CTCATCATCCCCACATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTTTAT
* *
23719 ATACCCAAAATTGGATTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAGCCC
66 ATACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCC
* * *
23784 CGTCCATATGAATTTTGTG-CTATCTAATAATTAAACAAAATACAATATTCAGTATCCCCAAACT
131 CGTCTATATGAATTTTGTGTC-ATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAACT
*
23848 GATATACTTTATACCCAAATAATTT
195 GATATACTTTATACCCAAATCATTT
* * * * * *
23873 CTCATCATCCCCAAATAATTATAAGCACCGTACCCAAAATTCATTAGAGATTGACATTTTTTCTT
1 CTCATCATCCCCACATAATCATATGCACCAT-CCCCAAATTCTTTAGAGATTGACATTTTTT-TT
* *
23938 ATATACCCAAAATTGGTTTTAAAAAGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAA
64 ATATACCCAAAATTGGCTTT-AAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAA
* * * * * ** *
24003 CCCCATATATATTAGTTTAT-TGTCATCTAATAATGAAACAAAACACAAAATTTAGTATCCCCAA
128 CCCCGTCTATATGAATTT-TGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCC-A
*
24067 AACCGATATACTTTATACCCAAATC
191 AACTGATATACTTTATACCCAAATC
24092 TTGTGATGCC
Statistics
Matches: 992, Mismatches: 90, Indels: 17
0.90 0.08 0.02
Matches are distributed among these distances:
217 1 0.00
218 569 0.57
219 229 0.23
220 54 0.05
221 22 0.02
222 91 0.09
223 26 0.03
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.36
Consensus pattern (219 bp):
CTCATCATCCCCACATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTTTAT
ATACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCC
CGTCTATATGAATTTTGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAACTG
ATATACTTTATACCCAAATCATTT
Found at i:23689 original size:437 final size:436
Alignment explanation
Indices: 22780--24091 Score: 2018
Period size: 437 Copynumber: 3.0 Consensus size: 436
22770 CTTGATATTA
* * *
22780 CTCATCATCCCCA-ACTAATCATAAGCACCATCCCCAAATTCATTAGACATTGACATTTTTTCTT
1 CTCATCATCCCCACA-TAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACA-TTTTT-TT
*
22844 ATATACCCAAAATTGGCTTTAAACGTGCTTTAATCCGTATTTTCATCCTAATTAATTGAATAAAC
63 ATATACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAAC
** * * * * * * **
22909 CTAGTCTAAATGAATTTAGTGCCATCTAATAATTAAACAACATGCAAAATTCAGTATTCCCAAGG
128 CCCGTCCATATGAATTTTGTG-CATCTAATAATTAAACAAAATGCAATATTCAGTATCCCCAAAC
*
22974 TGATATACTTTATACCCAAATCATTTCTCATCATCCCCACATAATCATATGCACCATCCCCAAAT
192 TGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAAT
* * *
23039 TCTTTAGAGATTGGCA-TTTTTTTATATACCCAAAATTGGGTTTAAACATGTTTTAATCTATATT
257 TCTTTAGAGATTGACATTTTTTTTATATACCCAAAATTGGGTTTAAACGTGTTTTAATCCATATT
*
23103 TTCATCCTAATTAATTGAATAAACCATGTCTATATGAATTTTGTGTCATTTAATAATTAAACAAA
322 TTCATCCTAATTAATTGAATAAACCATGTCTATATGAATTTTGTGTCATCTAATAATTAAACAAA
* *
23168 ATGTAAAATTCAGTATCTCCAAACTAATATACTTTATACCCAAATCATTT
387 ATGCAAAATTCAGTATCTCCAAACTGATATACTTTATACCCAAATCATTT
* *
23218 CTCATAATCCCCACATAATCATATGCATCATCCCCAAATTCTTTAGAGATTGACATTTTTTTATA
1 CTCATCATCCCCACATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTTATA
23283 TACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCC
66 TACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCC
23348 GTCCATATGAATTTTGTGTCATCTAATAATTAAACAAAATGCAATATTCAGTATCCCCAAACTGA
131 GTCCATATGAATTTTGTG-CATCTAATAATTAAACAAAATGCAATATTCAGTATCCCCAAACTGA
* *
23413 TATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAAACATATGCAACATCCCCAAATTCT
195 TATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCT
23478 TTAGAGATTGACATTTTTTTTATATACCCAAAATTGGGTTTAAACGTGTTTTAATCCATATTTTC
260 TTAGAGATTGACATTTTTTTTATATACCCAAAATTGGGTTTAAACGTGTTTTAATCCATATTTTC
* * *
23543 GTCCTAATTAATTTAATAAACCATGTCTATATGAATTTTGTGCCATCTAATAATTAAACAAAATG
325 ATCCTAATTAATTGAATAAACCATGTCTATATGAATTTTGTGTCATCTAATAATTAAACAAAATG
*
23608 CAAAATTCAGTATCTCCAAGCTGATATACTTTATACCCAAATCATTT
390 CAAAATTCAGTATCTCCAAACTGATATACTTTATACCCAAATCATTT
*
23655 CTCATCATCCCCACATAATCATATGCACCATCCCCAAATTTTTTAGAGATTGACATTTTTTTATA
1 CTCATCATCCCCACATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTTATA
* *
23720 TACCCAAAATTGGATTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAGCCCC
66 TACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCC
*
23785 GTCCATATGAATTTTGTGCTATCTAATAATTAAACAAAATACAATATTCAGTATCCCCAAACTGA
131 GTCCATATGAATTTTGTGC-ATCTAATAATTAAACAAAATGCAATATTCAGTATCCCCAAACTGA
* * * * *
23850 TATACTTTATACCCAAATAATTTCTCATCATCCCCAAATAATTATAAGCACCGTACCCAAAATTC
195 TATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATCATATGCACCAT-CCCCAAATTC
* * * *
23915 ATTAGAGATTGACATTTTTTCTTATATACCCAAAATTGGTTTTAAAAAGTGCTTTAATCCATATT
259 TTTAGAGATTGACATTTTTT-TTATATACCCAAAATTGGGTTT-AAACGTGTTTTAATCCATATT
*** * * * *
23980 TTCATCCTAATTAATTGAATAAACCCCATATATATTAGTTTAT-TGTCATCTAATAATGAAACAA
322 TTCATCCTAATTAATTGAATAAACCATGTCTATATGAATTT-TGTGTCATCTAATAATTAAACAA
** * * *
24044 AACACAAAATTTAGTATCCCCAAAACCGATATACTTTATACCCAAATC
386 AATGCAAAATTCAGTATCTCC-AAACTGATATACTTTATACCCAAATC
24092 TTGTGATGCC
Statistics
Matches: 803, Mismatches: 63, Indels: 13
0.91 0.07 0.01
Matches are distributed among these distances:
436 198 0.25
437 394 0.49
438 76 0.09
439 22 0.03
440 88 0.11
441 25 0.03
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.36
Consensus pattern (436 bp):
CTCATCATCCCCACATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTTATA
TACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCC
GTCCATATGAATTTTGTGCATCTAATAATTAAACAAAATGCAATATTCAGTATCCCCAAACTGAT
ATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTT
TAGAGATTGACATTTTTTTTATATACCCAAAATTGGGTTTAAACGTGTTTTAATCCATATTTTCA
TCCTAATTAATTGAATAAACCATGTCTATATGAATTTTGTGTCATCTAATAATTAAACAAAATGC
AAAATTCAGTATCTCCAAACTGATATACTTTATACCCAAATCATTT
Found at i:28679 original size:10 final size:10
Alignment explanation
Indices: 28653--28693 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
28643 GATTAAACAG
*
28653 AAAAAAGAAA
1 AAAAAACAAA
28663 AAGAAAACAAA
1 AA-AAAACAAA
28674 AAAAAACAAA
1 AAAAAACAAA
28684 AAAAAA-AAA
1 AAAAAACAAA
28693 A
1 A
28694 CTATACCATG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 4 0.14
10 16 0.55
11 9 0.31
ACGTcount: A:0.90, C:0.05, G:0.05, T:0.00
Consensus pattern (10 bp):
AAAAAACAAA
Found at i:30900 original size:4 final size:4
Alignment explanation
Indices: 30893--30939 Score: 51
Period size: 4 Copynumber: 11.5 Consensus size: 4
30883 TCATGGGCAT
* *
30893 GAAA GAAA GAAA GAAA GAAA GCAAA GGAAA AAAA AAAA GAAA -AAA GA
1 GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA GAAA GAAA GAAA GAAA GA
30940 TATCATTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
3 3 0.08
4 28 0.74
5 6 0.16
6 1 0.03
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:36867 original size:6 final size:6
Alignment explanation
Indices: 36856--36881 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
36846 TTCTTCTCAT
36856 CCCACG CCCACG CCCACG CCCACG CC
1 CCCACG CCCACG CCCACG CCCACG CC
36882 GTCATTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.69, G:0.15, T:0.00
Consensus pattern (6 bp):
CCCACG
Found at i:43537 original size:24 final size:24
Alignment explanation
Indices: 43510--43562 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
43500 AGCAGCTGCT
43510 GCCCTTTCTCGAGCCTCTACAGCA
1 GCCCTTTCTCGAGCCTCTACAGCA
* *
43534 GCCCTTTCTCGAGCCTCTGCAGCG
1 GCCCTTTCTCGAGCCTCTACAGCA
43558 GCCCT
1 GCCCT
43563 CTCCACGGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.11, C:0.43, G:0.21, T:0.25
Consensus pattern (24 bp):
GCCCTTTCTCGAGCCTCTACAGCA
Found at i:48011 original size:1 final size:1
Alignment explanation
Indices: 48007--48041 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
47997 TGCATTCAAT
48007 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
48042 GAGAGAGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.